Guillaume Fraux
Guillaume Fraux
See http://ambermd.org/FileFormats.php#topology and http://ambermd.org/prmtop.pdf for a complete specification. The tricky part will be that everything is specified as an arbitrary [fortran format](https://software.intel.com/en-us/fortran-compiler-developer-guide-and-reference-format-specifications). We would either need to parse the fortran...
This is an idea I had to improve atom-level properties. The issues I can see with the current system are: 1. since properties are stored on a per-atom basis, we...
http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file This is a simple extension of PDB, which could be supported by the same class. The main change is inversion of charge and atom type at the end of...
Since chemfiles is primarily intended to do file I/O, it could be nice to check its behavior upon I/O errors. I found two ways to check the behavior of code...
Examples at the bottom of http://chemfiles.org are not tested against the latest release, which mean they can fell out of sync with the code (see https://github.com/chemfiles/chemfiles.github.io/commit/fbf19e4a47e839e6e952fb3b4c3736f974ed69ed). As they can be...
Frame and atomic properties where added in #97, and used in #102 for the 'is_hetatm' property in the PDB format. But they could be used for more formats: every time...
One of the goals of chemfiles is to be easy to integrate with pre-existing codes. But currently, to use chemfiles as a reader/writer, one have to convert `Frame` from and...
Having a way to know whether a topology can change in a trajectory would be nice. Most of the time it does not, and reading the topology again and again...
We currently read the topology at every frame in the [TNG reader](https://github.com/chemfiles/chemfiles/blob/66e7ad1dfa109b9a095e356013c05af2c3b6b1bd/src/formats/TNG.cpp#L67). Instead, we should check if the topology can change (using the corresponding TNG flag), and only read it...
Getting the number of steps in a trajectory can be done at no cost for some formats (NetCDF), but might be very costly for other (XYZ). In big XYZ trajectory,...